The Commonwealth ombudsman has criticised parts of the Federal Government's controversial school chaplaincy program, saying the role of school chaplains is poorly defined and the Government has not provided adequate guidelines for schools taking part.

The Government is conducting an internal review of the program and says it is already implementing many of the ombudsman's recommendations.

But critics say the problems are more deep-seated than that and the entire scheme should be scrapped.

The Government has already put chaplains in more than 2,500 schools and is planning to expand the program by a further 1,000.

The chaplains are only allowed to offer pastoral care and support to students and are not permitted to proselytise.

But ombudsman Allan Asher says that is ambiguous and the Government needs to explain exactly what it means by proselytising.

"That's where some uncertainty has arisen because the scheme operators will all say, 'well, we don't do that' and parents will say, 'well, yes you do'," he said.

"But that's partly because I don't know really what the word is supposed to mean, and clearing that up might make it a lot easier for everyone."

Tim Mander, the chief executive of the Queensland Scripture Union, which employs chaplains in more than 600 schools, says chaplains already understand what they can and cannot do.

"We believe they are working with integrity; they've been working in schools for, in some states, up to 50 years," he said.

"This is a program that's well received and is well understood by the school communities. But if clarification is needed we would welcome that as well."

Mr Asher also argues the Government should introduce minimum qualification requirements for chaplains.

"Nobody's quite sure of what the minimum qualification should be for a chaplain," he said.

"By spelling that out, it makes it also clearer to everybody what sort of function they would carry. At the moment that's not the case and it would be rather helpful if that was done."

Mr Mander says his organisation has already introduced its own qualification requirements and the recommendation makes sense.

Religious incursion

The ombudsman has not delivered a verdict on the merits of the chaplaincy program itself.

He has criticised the complaints procedure and gives some examples of parents who are uncomfortable with what they view as a religious incursion into schools.

"What the Greens would like to see is the $222 million that's currently put aside for this program reworked into a program of student support, and that the people who are employed to support students firstly have the qualifications and secondly meet the needs of students in that particular school," she said.

"They shouldn't necessarily have to be attached to a religious organisation."

The scheme is also facing a High Court challenge. But Mr Mander says most parents have been very pleased with it.

"The complaint level against chaplaincy is less than 1 per cent of parents and students of which chaplains engage with," he said.

"They are an extremely minimal amount of enquiries coming through or complaints coming through.

"Overwhelmingly this has proven to be a successful program. It's endorsed by school principals, by teachers, by parents and by the students themselves."

Imprecise

School Education Minister Peter Garrett says the Government's internal review of the program has picked up some of the problems identified by the ombudsman.

He says Labor remains committed to school chaplains.

"It is the case that the ombudsman's come through with some useful recommendations on the chaplain's program, some of which are already in train and some of which will be implemented," he said.

"We broadly accept what the ombudsman has to say on a program that's very popular, but of course we want to see continually improve."

Mr Asher says he will be monitoring the Government's response.

"Sadly I think that their responses are themselves a bit like the scheme, a little imprecise," he said.

"We're going to look again in three months and publish in six months an update on just what has been implemented.

"By then the Government's own consultation process should be finished and we'd be looking for a much clearer set of actions."

The Government will hand down its internal review in the coming months.